Zinc in PDB 5zgv: Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit

All present enzymatic activity of Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit, PDB code: 5zgv was solved by H.Zhang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.678, 73.716, 66.605, 90.00, 98.40, 90.00
R / Rfree (%)	12.3 / 14.4

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit (pdb code 5zgv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit, PDB code: 5zgv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.8 occ:1.00 O A:OH303 2.0 9.6 1.0 NE2 A:HIS189 2.0 9.7 1.0 ND1 A:HIS122 2.0 9.7 1.0 NE2 A:HIS120 2.0 8.6 1.0 CD2 A:HIS189 3.0 8.9 1.0 CE1 A:HIS122 3.0 9.8 1.0 CE1 A:HIS120 3.0 8.6 1.0 CE1 A:HIS189 3.0 9.8 1.0 CG A:HIS122 3.1 9.2 1.0 CD2 A:HIS120 3.1 8.3 1.0 CB A:HIS122 3.4 8.5 1.0 ZN A:ZN302 3.4 9.5 1.0 O A:HOH425 3.7 27.6 1.0 SG A:CYS208 3.9 9.1 1.0 OD1 A:ASP124 4.1 10.3 1.0 CB A:CYS208 4.1 9.5 1.0 NE2 A:HIS122 4.1 10.4 1.0 ND1 A:HIS189 4.1 9.7 1.0 ND1 A:HIS120 4.1 8.7 1.0 CG A:HIS189 4.1 9.1 1.0 CD2 A:HIS122 4.2 9.4 1.0 O A:HOH429 4.2 26.6 1.0 CG A:HIS120 4.2 8.3 1.0 CG2 A:THR190 4.4 9.7 1.0 OD2 A:ASP124 4.6 10.1 1.0 CG A:ASP124 4.8 8.8 1.0 CA A:HIS122 4.9 8.2 1.0 O A:HOH587 4.9 18.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.5 occ:1.00 OD2 A:ASP124 2.0 10.1 1.0 O A:OH303 2.0 9.6 1.0 NE2 A:HIS250 2.0 10.1 1.0 SG A:CYS208 2.3 9.1 1.0 CG A:ASP124 3.0 8.8 1.0 CE1 A:HIS250 3.0 9.9 1.0 CD2 A:HIS250 3.0 9.5 1.0 OD1 A:ASP124 3.3 10.3 1.0 CB A:CYS208 3.4 9.5 1.0 ZN A:ZN301 3.4 8.8 1.0 O A:HOH425 3.8 27.6 1.0 ND1 A:HIS250 4.1 9.9 1.0 CB A:SER249 4.2 9.1 1.0 CG A:HIS250 4.2 9.4 1.0 NE2 A:HIS189 4.2 9.7 1.0 CB A:ASP124 4.3 8.4 1.0 NE2 A:HIS120 4.4 8.6 1.0 CE1 A:HIS189 4.4 9.8 1.0 CE1 A:HIS120 4.4 8.6 1.0 OG A:SER249 4.5 9.4 1.0 CA A:CYS208 4.6 9.4 1.0 CD A:LYS125 4.6 8.9 1.0 CE A:LYS125 4.6 8.9 1.0 CG A:LYS125 4.8 8.8 1.0 OG A:SER75 4.9 9.2 1.0 O A:HOH655 5.0 39.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:9.5 occ:1.00 O B:OH303 2.0 10.7 1.0 NE2 B:HIS189 2.0 10.6 1.0 ND1 B:HIS122 2.0 9.9 1.0 NE2 B:HIS120 2.1 9.4 1.0 CD2 B:HIS189 3.0 9.3 1.0 CE1 B:HIS122 3.0 10.2 1.0 CE1 B:HIS120 3.0 9.6 1.0 CE1 B:HIS189 3.0 10.4 1.0 CG B:HIS122 3.0 9.3 1.0 CD2 B:HIS120 3.1 8.9 1.0 CB B:HIS122 3.4 9.1 1.0 ZN B:ZN302 3.4 10.3 1.0 SG B:CYS208 3.9 9.7 1.0 CB B:CYS208 4.0 9.8 1.0 O B:HOH593 4.1 31.7 1.0 NE2 B:HIS122 4.1 10.5 1.0 ND1 B:HIS189 4.1 10.3 1.0 ND1 B:HIS120 4.1 8.9 1.0 CG B:HIS189 4.1 9.3 1.0 OD1 B:ASP124 4.1 10.4 1.0 CD2 B:HIS122 4.2 10.0 1.0 CG B:HIS120 4.2 8.9 1.0 CG2 B:THR190 4.5 10.1 1.0 OD2 B:ASP124 4.6 10.7 1.0 CG B:ASP124 4.8 9.4 1.0 CA B:HIS122 4.9 9.0 1.0 O B:HOH568 4.9 17.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 at PH8.0 (Tris) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:10.3 occ:1.00 O B:OH303 2.0 10.7 1.0 OD2 B:ASP124 2.0 10.7 1.0 NE2 B:HIS250 2.0 10.9 1.0 SG B:CYS208 2.3 9.7 1.0 CG B:ASP124 3.0 9.4 1.0 CE1 B:HIS250 3.0 10.9 1.0 CD2 B:HIS250 3.0 10.7 1.0 OD1 B:ASP124 3.2 10.4 1.0 CB B:CYS208 3.4 9.8 1.0 ZN B:ZN301 3.4 9.5 1.0 O B:HOH593 3.7 31.7 1.0 ND1 B:HIS250 4.1 11.0 1.0 CB B:SER249 4.1 9.3 1.0 CG B:HIS250 4.2 10.9 1.0 NE2 B:HIS189 4.2 10.6 1.0 CB B:ASP124 4.3 9.6 1.0 NE2 B:HIS120 4.4 9.4 1.0 CE1 B:HIS120 4.4 9.6 1.0 OG B:SER249 4.5 9.4 1.0 CE1 B:HIS189 4.5 10.4 1.0 CA B:CYS208 4.6 9.4 1.0 CD B:LYS125 4.7 9.5 1.0 CE B:LYS125 4.7 9.6 1.0 CG B:LYS125 4.8 9.7 1.0 OG B:SER75 5.0 10.9 1.0

H.Zhang, G.Ma, Y.Zhu, L.Zeng, A.Ahmad, C.Wang, B.Pang, H.Fang, L.Zhao, Q.Hao. Active-Site Conformational Fluctuations Promote the Enzymatic Activity of Ndm-1. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 30150473
DOI: 10.1128/AAC.01579-18